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- PDB-4rlf: Crystal structure of a benzoate coenzyme A ligase with p-Toluic a... -

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Basic information

Entry
Database: PDB / ID: 4rlf
TitleCrystal structure of a benzoate coenzyme A ligase with p-Toluic acid and o-Toluic acid
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE / Substrate Specificity / Kinetics
Function / homology
Function and homology information


acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-methylbenzoic acid / 4-METHYLBENZOIC ACID / Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsStrom, S. / Nosrati, M. / Thornburg, C. / Walker, K. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2015
Title: Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity.
Authors: Thornburg, C.K. / Wortas-Strom, S. / Nosrati, M. / Geiger, J.H. / Walker, K.D.
History
DepositionOct 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references / Structure summary
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Benzoate-coenzyme A ligase
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,94914
Polymers112,6672
Non-polymers1,28112
Water9,800544
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A: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7905
Polymers56,3341
Non-polymers4564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1599
Polymers56,3341
Non-polymers8258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.716, 95.366, 95.785
Angle α, β, γ (deg.)90.00, 104.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Benzoate-coenzyme A ligase


Mass: 56333.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: badA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q93TK0
#2: Chemical ChemComp-3SK / 2-methylbenzoic acid


Mass: 136.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O2
#3: Chemical ChemComp-4MA / 4-METHYLBENZOIC ACID / P-METHYLBENZOIC ACID


Mass: 136.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 % PEG 3350, 0.1 M Tris pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 96640 / % possible obs: 95.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 22.18 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.06 / Net I/σ(I): 17.8
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.52 / Rsym value: 0.574 / % possible all: 72.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V7B

2v7b


Resolution: 1.73→32.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.479 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19525 5121 5 %RANDOM
Rwork0.1594 ---
obs0.16121 96612 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.318 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7792 0 88 544 8424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198102
X-RAY DIFFRACTIONr_bond_other_d0.0020.027614
X-RAY DIFFRACTIONr_angle_refined_deg1.9661.97311048
X-RAY DIFFRACTIONr_angle_other_deg0.952317478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60151041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09422.879323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.403151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741554
X-RAY DIFFRACTIONr_chiral_restr0.1580.21230
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021851
X-RAY DIFFRACTIONr_mcbond_it2.0562.0734146
X-RAY DIFFRACTIONr_mcbond_other2.0512.0734145
X-RAY DIFFRACTIONr_mcangle_it2.7783.0995181
X-RAY DIFFRACTIONr_mcangle_other2.7783.0995182
X-RAY DIFFRACTIONr_scbond_it2.962.3263956
X-RAY DIFFRACTIONr_scbond_other2.962.3263957
X-RAY DIFFRACTIONr_scangle_other4.3513.3775864
X-RAY DIFFRACTIONr_long_range_B_refined5.64117.3679224
X-RAY DIFFRACTIONr_long_range_B_other5.56217.1169033
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 294 -
Rwork0.27 5320 -
obs--72.09 %

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